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FOXBOROUGH  Patriots coach Bill Belichick spent the week telling anyone who would listen that the Indianapolis Colts, despite being winless, were a formidable opponent that would pose a challenge to the Patriots.

The Colts did show flashes, keeping the score close in the first quarter and rallying for a flurry of fourth-quarter points, but the Patriots dominated in between and posted a 31-24 victory at Gillette Stadium.

"We've obviously got to do a better job of finishing off the game," said Patriots coach Bill Belichick. "We'll work on that."

Tight end Rob Gronkowski scored three touchdowns and quarterback Tom Brady hit 29 of 38 passes for 293 yards to lead New England, which improved to 9-3.

Gronkowski caught two touchdown passes and ran for a third after catching a lateral pass from Brady. He finished with five receptions for 64 yards.

Right out of the gate, Indianapolis (0-12) put itself in a hole, a trend throughout the afternoon for the visitors. On no fewer than three drives, one of its offensive linemen was flagged for a penalty on the first or second snap of the possession, giving an anemic offense and even longer field to deal with.

The Patriots had their own offensive struggles early, but once the switch was made to a no-huddle scheme, Brady worked with surgical precision.

"Offensive football is all 11 guys being on the same page. I thought we definitely did that at times today," Brady said. "The middle part of the game was awesome. We just came up third, fourth and a quarter of a yard short on the one and never got out of the long yardage situation there in the second to last drive. Well try to do a better job of that next week. "

The score was tied 3-3 early in the second quarter after a 19-play drive by the Colts that resulted in an Adam Vinatieri 31-yard field goal  Vinatieri, the hero of several New England playoff games, including two Super Bowls, was booed by the Gillette Stadium crowd  but there wasnt much else positive that happened for the Colts from that point.

Brady played well into the fourth quarter despite a lopsided score -- the Patriots led 31-3 after the third quarter -- and just about the only negative came in the third quarter when the games official scorer turned his third passing touchdown of the day into a rushing one when it was deemed the play was a lateral.

The call was significant because had the it stood up as a passing touchdown, it would have been Gronkowskis 14th receiving touchdown of the season, giving him an NFL record for touchdowns by a tight end. It also would have been Bradys 292d career passing TD, which would have put him alone at sixth-place all-time in that category.

But 14 touchdowns for Gronkowski  13 receiving and one rushing  is still a record for a tight end in a season. Brady remains tied with Warren Moon in sixth place at 291.

The Colts made things interesting by rallying for 21 points in the fourth quarter, and they attempted an onside kick with less than a minute remaining that could have set up a potential game-tying touchdown.

But Deion Branch recovered the kick with 34 seconds left and the Patriots ran out the clock.

Patriots players were upset with how the game ended.

"It's a mindset," said defensive end Andre Carter, who has become the face of the team's nascent pass rush. "It's just knowing what you have to do and just trying to go out there and execute. Unfortunately toward the end, toward the final stretch of the game, Indy was just able to make big plays, and that's something we've got to eliminate."

Indianapolis announced on Tuesday that quarterback Curtis Painter would be benched, and UConn product Dan Orlovsky made his first start since 2008 with the Lions. Peyton Manning, who has missed the season due to neck surgery, was on hand at the game, wearing an earpiece on the sideline, listening to the coaching chatter and play-calling; before kickoff, he was signing autographs for Colts fans on hand as well as Pats fans.

Orlovsky had his moments, but most of them came after the game was out of reach for the Colts. He too completed more than 75 percent of his passes, and converted four third-down chances on Indianapolis first scoring drive before a false-start flag on former Pat Quinn Ojinnaka and a Rob Ninkovich sack forced it to kick a field goal.

Orlovsky had 33- and 12-yard touchdown passes to Pierre Garcon in the fourth quarter. Donald Brown, another UConn product, ran five yards for the Colts' other touchdown.

"We felt confident going into the game that if we stayed patient we could move the ball. Thats kind of what happened. Throughout the first half we were able to do some decent things. In the second half, [we were] kind of forced into making some plays. The defense did a good job getting some stops and the offense did a good job of picking up some of the stuff they were trying to do and making plays in the outside. So, we fell short. I wish we had more time on the clock," Orlovsky said.

The Patriots' defense was booed off the field following Pierre Garcon's touchdown with 36 seconds remaining in the fourth quarter that made the score 31-24 in favor of the home team. New England had done enough to wrap up the victory in the game's middle 30 minutes, but the home crowd was unhappy with how they finished up the final fifteen. The Patriots gave up the final 21 points of the game to turn a blowout into something different.

"It's kind of disappointing, to be honest with you," Patriots linebacker Jerod Mayo said. "Even though it's a win, you just want to win games in the National Football League, it's just so disappointing to finish like that, man."

The Patriots started receiver Matthew Slater at safety and he played nearly every snap, although he did not look comfortable. He did force a second-half fumble that was recovered by Kyle Arrington.

Cornerback Devin McCourty returned to action for New England after missing the previous two games with a separated shoulder. Safety Patrick Chung sat out again with a foot injury. It is expected he will make his return next week against the Redskins.